You are correct (had a >= instead of >). I've put the corrected file here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/flac_customize.m
Copy it into $FREESURFER_HOME/fsfast/toolbox
doug
On Sun, 13 Apr 2008, Lionel zorzevic wrote:
Thanks,
It seems to work properly (now TPEF files in seconds are accepted), although I noticed the last volume could not be excluded (TP 267 out of 90 volumes i.e. 0 to 89, TR 3s still fails). As far as I don't know what lies behind Freesurfer Time-point exclusions, I hypothesize this could be due to the procedure itself (e.g. time-depent linear interpolation of excluded volumes) rather than a bug. Is that right?
thank again.
-- L. Landré
Date: Wed, 9 Apr 2008 16:41:13 -0400> From: greve@nmr.mgh.harvard.edu> To: zorzevic@hotmail.com> CC: freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Time-point exclusion failure in selxavg3-sess> > > The values in the file are supposed to be time in sec (like the paradigm > file). However, I noticed that I had a bug that prevented the time point > file from having any effect. I have fixed this in our local dev and > stable versions, and it will be in the next stable release. However, if > you want it before then, I have created a patch here:> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fsfast.patch.tar.gz> > Here's what to do:> > cd $FREESURFER_HOME/fsfast/toolbox> > # Back up the old files:> mkdir -p temp> cp fast_ldanaflac.m fast_selxavg3.m flac_customize.m flac_desmat.m > flac_ev_parse.m temp> > # Install patch> tar xvfz fsfast.patch.tar.gz> > # I've tested it, but (obviously, things can go wrong). If so, you can > restore from your backup:> cd $FREESURFER_HOME/fsfast/toolbox> cp temp/* .> > Let me know how it goes> > doug> > > Lionel zorzevic wrote:> > >Dear Dr Greve,> >> >> >As I tried to introduce time-point exclusions in an analysis, selxavg3-sess returned the following error:> >> >> >ERROR: time points in /.automount/space3/newfspace/070630_METRAPI_TM05/bold/001/spike.txt exceed nframes (91)> >> >> >91 corresponds to run length in TR (but not in seconds)> >> >Just to check, I wrote a TPEF file with numbers inferior to 91, and selxavg3-sess succeeded.> >> >Is it to say TPEF files are now to be written in terms of TR , not in seconds?> >> >> >Thanks by advance, and sorry for the double post.> >> >--> >Lionel Landré,> >UMR-CNRS 6234> >> >_________________________________________________________________> >Créez votre disque dur virtuel Windows Live SkyDrive, 5Go de stockage gratuit !> >http://www.windowslive.fr/skydrive/%3E >_______________________________________________> >Freesurfer mailing list> >Freesurfer@nmr.mgh.harvard.edu> >https://mail.nmr.mgh.harvard.edu/mailm!
an/listi nfo/freesurfer> >> >> > > >> > -- > Douglas N. Greve, Ph.D.> MGH-NMR Center> greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 > Fax: 617-726-7422> > In order to help us help you, please follow the steps in:> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >
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